- recipe nomadic
Mobile sequencing and analysis in real-time
- Homepage:
- Developer docs:
- License:
MIT
- Recipe:
Nomadic is a real-time bioinformatics pipeline and dashboard for nanopore sequencing data. While sequencing is still ongoing, it performs read mapping and sample quality control, as well as variant calling and annotation. This information is displayed in real-time to a graphical dashboard that has interactive features.
- package nomadic¶
- Versions:
0.8.0-0,0.7.2-0,0.7.1-0,0.7.0-0,0.6.0-0,0.5.0-0,0.4.0-0- Depends:
on bcftools
>=1.20on bedtools
on click
on dash
on delve-bio
0.2.*on i18nice
on minimap2
on numpy
on openpyxl
on pandas
on platformdirs
on pysam
on python
>=3.10on pyyaml
on rsync
on samtools
>=1.20on seaborn
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install nomadic
to add into an existing workspace instead, run:
pixi add nomadic
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install nomadic
Alternatively, to install into a new environment, run:
conda create -n envname nomadic
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/nomadic:<tag>
(see nomadic/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/nomadic/README.html)
